report_orthologs: Report orthologs

In neurogenomics/orthogene: Interspecies gene mapping

Report orthologs

Description

Identify the number of orthologous genes between two species.

Usage

report_orthologs(
  target_species = "mouse",
  reference_species = "human",
  standardise_genes = FALSE,
  method_all_genes = c("homologene", "gprofiler", "babelgene"),
  method_convert_orthologs = method_all_genes,
  drop_nonorths = TRUE,
  non121_strategy = "drop_both_species",
  round_digits = 2,
  return_report = TRUE,
  ref_genes = NULL,
  mc.cores = 1,
  verbose = TRUE,
  ...
)

Arguments

target_species	Target species.
reference_species	Reference species.
standardise_genes	If TRUE AND gene_output="columns", a new column "input_gene_standard" will be added to gene_df containing standardised HGNC symbols identified by gorth.
method_all_genes	R package to to use in all_genes step: "gprofiler" : Slower but more species and genes. "homologene" : Faster but fewer species and genes. "babelgene" : Faster but fewer species and genes. Also gives consensus scores for each gene mapping based on a several different data sources.
method_convert_orthologs	R package to to use in convert_orthologs step: "gprofiler" : Slower but more species and genes. "homologene" : Faster but fewer species and genes. "babelgene" : Faster but fewer species and genes. Also gives consensus scores for each gene mapping based on a several different data sources.
drop_nonorths	Drop genes that don't have an ortholog in the output_species.
non121_strategy	How to handle genes that don't have 1:1 mappings between input_species:output_species. Options include: "drop_both_species" or "dbs" or 1 : Drop genes that have duplicate mappings in either the input_species or output_species (DEFAULT). "drop_input_species" or "dis" or 2 : Only drop genes that have duplicate mappings in the input_species. "drop_output_species" or "dos" or 3 : Only drop genes that have duplicate mappings in the output_species. "keep_both_species" or "kbs" or 4 : Keep all genes regardless of whether they have duplicate mappings in either species. "keep_popular" or "kp" or 5 : Return only the most "popular" interspecies ortholog mappings. This procedure tends to yield a greater number of returned genes but at the cost of many of them not being true biological 1:1 orthologs. "sum","mean","median","min" or "max" : When gene_df is a matrix and gene_output="rownames", these options will aggregate many-to-one gene mappings (input_species-to-output_species) after dropping any duplicate genes in the output_species.
round_digits	Number of digits to round to when printing percentages.
return_report	Return just the ortholog mapping between two species (FALSE) or return both the ortholog mapping as well a data.frame of the report statistics (TRUE).
ref_genes	A table of all genes for the reference_species. If NULL (default), this will automatically be created using all_genes.
mc.cores	Number of cores to parallelise each target_species with.
verbose	Print messages.
...	Arguments passed on to convert_orthologs gene_df Data object containing the genes (see gene_input for options on how the genes can be stored within the object). Can be one of the following formats: matrix : A sparse or dense matrix. data.frame : A data.frame, data.table. or tibble. codelist : A list or character vector. Genes, transcripts, proteins, SNPs, or genomic ranges can be provided in any format (HGNC, Ensembl, RefSeq, UniProt, etc.) and will be automatically converted to gene symbols unless specified otherwise with the ... arguments. Note: If you set method="homologene", you must either supply genes in gene symbol format (e.g. "Sox2") OR set standardise_genes=TRUE. gene_input Which aspect of gene_df to get gene names from: "rownames" : From row names of data.frame/matrix. "colnames" : From column names of data.frame/matrix. <column name> : From a column in gene_df, e.g. "gene_names". gene_output How to return genes. Options include: "rownames" : As row names of gene_df. "colnames" : As column names of gene_df. "columns" : As new columns "input_gene", "ortholog_gene" (and "input_gene_standard" if standardise_genes=TRUE) in gene_df. "dict" : As a dictionary (named list) where the names are input_gene and the values are ortholog_gene. "dict_rev" : As a reversed dictionary (named list) where the names are ortholog_gene and the values are input_gene. input_species Name of the input species (e.g., "mouse","fly"). Use map_species to return a full list of available species. output_species Name of the output species (e.g. "human","chicken"). Use map_species to return a full list of available species. agg_fun Aggregation function passed to aggregate_mapped_genes. Set to NULL to skip aggregation step (default). mthreshold Maximum number of ortholog names per gene to show. Passed to gorth. Only used when method="gprofiler" (DEFAULT : Inf). method R package to use for gene mapping: "gprofiler" : Slower but more species and genes. "homologene" : Faster but fewer species and genes. "babelgene" : Faster but fewer species and genes. Also gives consensus scores for each gene mapping based on a several different data sources. as_sparse Convert gene_df to a sparse matrix. Only works if gene_df is one of the following classes: matrix Matrix data.frame data.table tibble If gene_df is a sparse matrix to begin with, it will be returned as a sparse matrix (so long as gene_output= "rownames" or "colnames"). sort_rows Sort gene_df rows alphanumerically. gene_map A data.frame that maps the current gene names to new gene names. This function's behaviour will adapt to different situations as follows: gene_map=<data.frame> : When a data.frame containing the gene key:value columns (specified by input_col and output_col, respectively) is provided, this will be used to perform aggregation/expansion. gene_map=NULL and input_species!=output_species : A gene_map is automatically generated by map_orthologs to perform inter-species gene aggregation/expansion. gene_map=NULL and input_species==output_species : A gene_map is automatically generated by map_genes to perform within-species gene gene symbol standardization and aggregation/expansion. as_DelayedArray Convert aggregated matrix to DelayedArray. input_col Column name within gene_map with gene names matching the row names of X. output_col Column name within gene_map with gene names that you wish you map the row names of X onto.

Value

A list containing:

• map : A table of inter-species gene mappings.

• report : A list of aggregate orthology report statistics.

If >1 target_species are provided, then a table of aggregated report statistics concatenated across species will be returned instead.

Examples

orth_fly <- report_orthologs(
    target_species = "fly",
    reference_species = "human")

neurogenomics/orthogene documentation built on Jan. 30, 2024, 4:44 a.m.